SPLATCHE v1.1 User Manual - Population Genetics CMPG Lab
Contents
1. tab our space character 1 Name of the population from which the sample has been drawn 2 Number of genes belonging to that sample 3 amp 4 Geographic location of the population latitude and longitude SPLATCHE will determine automatically in which particular deme falls the coordinates of the population The coordinates must belong to the geographical surface defined in the header file Example of a genetic input file sam for 6 samples in Africa 4 4 Output files on Figure 4 1 Various kinds of genetic output files can be generated by SPLATCHE 4 4 1 Arlequin files The genetic data generated by one simulation are directly output in an ARLEQUIN project file with the extension arp This file format allows one to compute the data using the ARLEQUIN software in order to obtain different statistics see ARLEQUIN manual Schneider et al 2000 for more details If more than one simulation is performed using one demographic simulation which is usually the case then an ARLEQUIN batch file with extension arb is also generated listing all simulated files and allowing one to compute statistics on the whole set of simulated files Note also that the 19 SPLATCHE v1 1 User Manual ARLEQUIN software has a file conversion utility for exporting input data files into several other format like BIOSYS PHYLIP or GENEPOP so that files produced by SPLATCHE could be also analyzed by these softwares after2. settings_square txt 1 Open Settings 2 Save Settings Simulation duration sec 3 Demography Initial Density Overflo FA Number of Generation Fu 5 Growth rate LS sain rate Allow density overflow Environment Friction Dynamism I Allow dynamic environments Vegetation Roughness Both r Vizualize Tiol tables 12 seil 10 table Outputs every 50 genet 13 M generate BMP of J number of migrants Iv ir M population density population density 17 19 F occupation generate ASCII raster of F occupation Build World A RUN Show results Figure 3 1 General Setting panel The numbers correspond to a description in the text SPLATCHE v1 1 User Manual 3 3 1 General Settings file name location of the settings file txt See chapter 3 4 2 for the full description of a settings file Buttons allowing to open a settings file or to save a settings file Progress bar showing the remaining computation time of a current simulation The duration of a simulation in seconds is also given at the end of the computation 3 3 2 Demography related parameters 4 Drop down menu allowing to choose among the three available demographic models Number of simulated generations Le Growth rate used in the demographic models This is the net growth rate used in the log
3. 9 3 4 4 Dynamic simulations and conversion tables to obtain K and F 10 3 5 Graphical outputs window ER A SE nt ae 12 3 6 Demographic outputs window nn a LEE Nate 14 Ae Genetic module se teediiad ss tesseesateiesd sas reen MEN en nn td 15 4 1 Principles Sn ee st nes ee ln ee ee A ne ne 15 42 Settings pan l eion SR ee SR E Mn cloacal aa Ald 16 4 2 1 LG J 0 22 I E ieee Beery E E E PPO EEE Come tt RCOTIPRPESEE CAR ETC 16 4 2 2 Mutation model SDECHICIT S mers nine metre 17 4 2 3 G netie data sissies ida as ine e Ea ESE EE dt 18 4 3 Taput TAGS en Se nn Re E SR 19 4 3 1 GERS HS samples haca o nr eee 19 44 Output files ini in inside RE AEE E 19 SPLATCHE v1 1 User Manual 4 4 1 PVE QUITS Sis RAR en dt sees 19 4 4 2 Nexus less E E E dede E einer renier EA 20 4 4 3 Coalescence distribution files ccccccccccccceceessssecececececeesessaeeeeeceeseeenees 20 4 4 4 Coalescent trees files 20 4 4 5 MRCA HSE en dre ne 20 4 4 6 Tree MES tennis a on ire init Dis irnilet ie site 20 4 4 7 Oth r PCS sos cen rien ie nie rai ere et E E E iets dosette 21 5 Ackjowledeements Lan tiem igse tanita tate lsc En een 21 6 WDownload sitess 5c c 28 ek PRE er er ee nee RON ne le ord 21 Te VRETETENCES HT le ne sante ete Ut o at Die 21 3 Demographic and spatial expansion module 3 1 Principles The demographic and spatial expansion module allows to simulate a demographic and spatial expansion from one or many initial populations T
4. Genetic simulations are always preceded by a demographic simulation Indeed a genetic simulation uses the demographic information stored in the data base generated during the demographic phase The genetic phase is based on the coalescent theory initially described by Kingman Kingman 1982 Kingman 1982 and developed in other papers Ewens 1990 Hudson 1990 Donnelly and Tavar 1995 This theory allows the reconstruction of the genealogy of a series of sampled genes until their most recent common ancestor MRCA For neutral genes the genealogy essentially depends on the demographic factors that have influenced the history of the populations from whom the genes are drawn The implementation of the coalescent theory is a modified version of SIMCOAL Excoffier et al 2000 The principal difference with SIMCOAL is that the demographic information used by genetic simulations does not come from the migration matrix and historical events anymore but from the data base generated during the demographic simulation The genetic simulation itself follows the procedure described in Excoffier et al 2000 and consists in two phases 1 Reconstruction of the genealogy The reconstruction of the genealogy is independent on the mutational process Basically a number n of genes is chosen These genes are only identified by their number and they have no genetic variability during this first phase All the n genes are associated with a geogr
5. for the simulation of molecular data in interconnected populations with arbitrary demography J Heredity 91 506 510 Hudson R 1990 Gene genealogies and the coalescent process Oxford Oxford University Press Jin L and M Nei 1990 Limitations of the evolutionary parsimony method of phylogenetic analysis Mol Biol Evol 7 82 102 Jukes T and C Cantor 1969 Evolution of protein molecules Mamalian Protein Metabolism H N Munro New York Academic press 21 132 21 SPLATCHE v1 1 User Manual Kimura M 1980 A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences J Mol Evol 16 111 120 Kimura M and W H Weiss 1964 The stepping stone model of genetic structure and the decrease of genetic correlation with distance Genetics 49 561 576 Kingman J F C 1982 The coalescent Stoch Proc Appl 13 235 248 Kingman J F C 1982 On the genealogy of large populations J Appl Proba 19A 27 43 Page R D M 1996 TREEVIEW An application to display phylogenetic trees on personal computers Comput Appl Biosci 12 357 358 Ray N 2003 Mod lisation de la d mographie des populations humaines pr historiques l aide de donn es environnementales et g n tiques D partment d Anthropologie Gen ve Universit de Gen ve available at http www unige ch cyberdocuments theses2003 RayN meta html
6. number of emigrants M in any of the four directions is then computed as SPLATCHE v1 1 User Manual 1 4 1 F X Dr where F is the friction of the deme in direction i north south east or west and M floor mN 0 floor means that the fractional part of the number is truncated This model always gives a total number of emigrants which is a multiple of four Model 2 Migration model with absolute number of emigrants Same as Model 1 but the fractional part of M is not truncated Instead a multinomial distribution is used to split M emigrants to the neighboring demes see Ray 2003 This ensures that there are always M emigrants that are sent The drawback of this technique is that it requires the drawing of random numbers which increases the time required for a simulation Model 3 Stochastic migration model with absolute number of emigrants Same as Model 2 but the deme size N and the number of emigrants M vary stochastically and are drawn from a Poisson distribution centered around their initial value SPLATCHE v1 1 User Manual 3 3 General Settings panel The General Settings panel is the primary panel to set the demographic parameters and to launch a demographic simulation A screenshot of this panel is shown in Figure 3 1 A description of each component of this panel is given in the following sub chapters SPLATCHE lol x General Settings Demographic outputs Genetic simulations Settings file
7. 331 Ray N M Currat et al 2003 Intra deme molecular diversity in spatially expanding populations Molecular Biology and Evolution 20 1 76 86 Schneider S D Roessli et al 2000 Arlequin a software for population genetics data analysis User manual ver 2 000 Geneva Genetics and Biometry Lab Dept of Anthropology University of Geneva 29
8. SPLATCHE v1 1 User Manual SPLATCHE v1 1 USER MANUAL 1 Introduction The goal of this user manual is to describe the technical aspects of the software SPLATCHE version 1 1 This manual complements the article from Currat Ray and Excoffier published in Molecular Ecology Notes Currat et al 2004 Further details on the methodology can also be found in Ray 2003 and Currat 2004 The official webpage for SPLATCHE is found at http cmpg unibe ch software splatche What s new in version 1 1 implementation of multiple origins see chapter 3 4 1 minor bug fix 2 Contents Li AIP OCMC ON 2A AC EN SIE I ENS AE Re T 1 2 ME OTS INS annn a a a E E E ges ces Mase 1 3 Demographic and spatial expansion module ee eee eeeee cence cneeceeeeseeeeseecsaeeneensees 2 3 1 Principles Sd ee a TR Re nn ne a ee 2 3 2 Available demographic models 0e si RS De eae 2 3 3 General Settings DANCE EN RS aa a e ian 4 3 3 1 GEn ral nesine r eee ee a er ene eo ne ree 5 3 3 2 Demography related parameters eeccecssccecsecceceseceeseeceeseceeseceesaeeees 5 3 3 3 Environment related parameters sd asrennnmeaisenieeeneenat nriss 5 3 3 4 O tp t parameters Pa RE E E A E 6 3 3 5 Main buttons usure een ainsi 6 DAD a VPC Tales Re ns A Re MN nent 7 3 4 1 Initial density and origin location s 7 3 4 2 SONO S MES Ra A ETA E E T E T 8 3 4 3 ASCII format for environmental data
9. aphic position in the virtual world where the demography is simulated These genes could belong to different demes in the world Then going backward in time the genealogy of these genes is reconstructed until their most recent common ancestor MRCA in the following way Going backward in time at each generation two events can occur Coalescent event if at least two genes are in the same deme they have a probability to have a common ancestor at the preceding generation a coalescent event This probability depends on the population size of the deme where the genes are located Each pair of genes has a probability 1 Ni of coalescence if N is the number of haploid individual in the deme i If there are ni genes on the deme then the probability of one coalescent event becomes nj ni 1 2N Only one coalescent event is allowed per deme and per generation see Ray ef al 2003 for a discussion about this assumption 15 SPLATCHE v1 1 User Manual Migration Each gene could have arrived with an immigrant from a different deme When going backward in time it means that the gene could leave the current deme with the immigrant So the probability of migration from a deme i to a deme j for a gene depends on the number of individuals that have arrived from deme j to deme i at this generation For each gene belonging to the deme i the probability of migration from deme j is equal to m N where mj is the number of immigrants from deme
10. file conversion 4 4 2 Nexus files Two other types of file produced by Friction are compatible with the NEXUS file format for each simulation a file with paup extension could be generated This file lists all the simulated genes together with their true genealogical structure This file can be analyzed with David Swofford s PAUP software 1999 A PAUP batch file with extension baf is also generated 4 4 3 Coalescence distribution files A bitmap representing the spatial distribution of the coalescent events for all the simulations joined is automatically created with the _TotNumCoal bmp termination This bitmap can also be visualized through the button Draw Coalescence 15 on Figure 4 1 on the interface When checking the coalescence checkbox 16 on Figure 4 1 similar bitmaps of the spatial distribution of coalescent events are generated for every simulations with the _NumCoal bmp termination The times for each coalescent event and each simulation are listed on a file with coal extension Those times are given in generation units with larger numbers corresponding to the end time of the simulation 4 4 4 Coalescent trees files By checking the checkbox coalescent trees 16 on Figure 4 1 it is possible to generate for each simulation a bitmap representing the genealogical links between each node of the coalescence tree laid out spatially Those files are terminated with Coa
11. g to what type category of vegetation belongs each deme The second dataset is the roughness dataset defining continuous friction values such as friction computed from topography This format of the environmental dataset is composed of a header first six lines containing information on the file then a matrix of values in rows and columns This format is identical to the ASCII grid format output by the ArcView GIS package The header information is as follow ncols number of columns nrows number of rows xllcorner longitude coordinate of the lower left dem yllcorner latitude coordinate of the lower left dem cellsize width of a dem cell size in same units than the coordinates SPLATCHE v1 1 User Manual NODATA_value value indicating than a deme must not be considered like sea Example of an environmental dataset ncols nrows xllcorner 19 845388 yllcorner 36 897187 cellsize 0 83 NODATA_value 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 7 7 7 3 4 4 Dynamic simulations and conversion tables to obtain K and F It is possible in SPLATCH to do dynamic simulations A dynamic simulation allows variation of carrying capacity and or friction value at different time during the course of a simulation In order to set at what time the changes occur different files are
12. he generation of ASCII raster files a Je O1 Main buttons 2 Button to build a world It is during a building process that memory space is allocated and that carrying capacity and friction values are computed for each 2 deme 21 Button to launch a simulation If this button is grayed out it means that the world needs to be built or rebuilt 2 Button to show the graphical output window iR SPLATCHE v1 1 User Manual 3 4 Input files 3 4 1 Initial density and origin location s VERSION 1 1 this file format has changed and is not backward compatible with SPLATCHE 1 0 A file called dens_init txt in the examples is used to specify the place s of origin of the simulated population This file contains a first line indicating the number of origins followed by one line per origin and finally by a legend Each line per origin contains 6 fields separated by tab or space character 1 Name of the source population do not use space characters for this name 2 Size of the source population in number of effective haploid individuals 3 amp 4 Geographic coordinates of the population source latitude and longitude SPLATCHE will determine itself in which particular deme corresponds the coordinates of the population Coordinates must belong to the geographical surface defined in the header of the environmental files Coordinates do not need to be in a particular units e g decimal degrees bu
13. he simulation uses discrete time and space The unit of time is the generation while the unit of the 2D space is a cell also called a deme Each deme has the same size and can be considered as a homogeneous subpopulation The spatial model used in SPLATCHE is the 2D stepping stone model Kimura and Weiss 1964 which defines a regularly spaced array of demes Each deme undergoes an independent population growth and can exchange emigrants with its four direct neighboring demes Each deme is also considered as a sub unit of the environment The environment can influence the local demography through its carrying capacity maximum number of individuals and its friction facility to migrate through These two environmental characteristics can be defined for the entire array of demes through input maps Variations through time of carrying capacity and or friction values are also possible which is defined as a dynamic environment 3 2 Available demographic models The logistic population growth of each deme follows a standard logistic curve of the form K N Na EN ier K where K is the carrying capacity and r is the growth rate For the migration part of the demography three models are available in SPLATCH Model 1 Migration model with even number of emigrants The number of emigrants M from a deme is computed for each generation as M mN where m is the migration rate and N is the population density of the deme at generation t The
14. istic growth phase Migration rate used in the demographic models The migration rate m is the fraction of the deme population that will emigrate at each generation For a deme population of size N the number of emigrants is therefore equal to N m at each generation F1 Checkbox to allow the initial density overflow If this checkbox is switched on and the size of the initial population exceeds the carrying capacity of the deme the initial population is spread over neighboring demes until all the individuals are placed in a deme The overflow function fills a deme at carrying capacity before using neighboring demes If this checkbox is switched off the size of the initial population is always the size set in the initial density file see chapter 3 4 1 even if this size exceeds the carrying capacity in this case the deme size is regulated downward by the logistic equation 3 3 3 Environment related parameters Radio button allowing to choose how the friction values are computed When vegetation or roughness is chosen friction values are only computed from the corresponding input data set see chapter 3 4 3 If both is chosen friction values are computed by taking for each deme the mean value between the friction value from the vegetation data set and the friction value from the roughness data set SPLATCHE v1 1 User Manual Button allowing to open the friction corresponding table see chapter 3 4 4 for a description of this tab
15. j to deme i during the demographic phase All the deme sizes and the numbers of immigrant between demes are taken from the database generated during the demographic simulation 2 Generation of the genetic diversity The second phase of a genetic simulation consists in generating the genetic diversity of the samples This operation is done by adding independent mutations on all branches of the genealogy assuming a uniform and constant Poisson process At the end of this process all sampled genes have a specific genetic identity The genetic process is entirely stochastic so many genetic simulations have to be performed for each demographic simulation in order to obtain meaningful statistics We recommend at least 1 000 simulations per demographic scenario The coalescent backward approach does not generate the history of the whole population but only that of sampled genes and their ancestors Thus this approach is much less demanding in terms of memory and computing time It allows the simulation of complex demographic scenarios within a very broad geographical and temporal framework 4 2 Settings panel Various parameters must be defined before launching a genetic simulation The number of parameters can be seen in Figure 4 1 4 2 1 General Sample file name location of the sam file Number of simulations to be carried out Maximum number of generations after which the process stop if the genealogy has not reached the MRCA Ref
16. lTree_ bmp 4 4 5 MRCA files SPLATCHE gives information on the localization and timing of the Most Recent Common Ancestor MRCA of the totality of genes sampled and the MRCA of each of the various samples A file with the termination _MRCADensity bmp is automatically generated and is a bitmap of the spatial distribution of MRCA for all the simulations added together These maps can also be visualized through the button Draw MRCA 15 on Figure 4 1 on the interface Similar bitmaps with the MRCAPopDensity bmp termination are generated for each sample The Time to the Most Recent Common Ancestor TMRCA for the whole tree and for each sample are also listed in a file with the tmrca extension The TMRCA are given in generation units with larger numbers corresponding to the end time of the simulation 4 4 6 Tree files Two files with the trees extension are automatically produced and list all the simulated trees with branch lengths expressed either 7 in units of generations scaled by the population size N and therefore representing the true coalescent history of the sample of genes or ii in units of average number of substitutions per site and therefore 20 SPLATCHE v1 1 User Manual representing the realized mutational tree These two files could be visualized with the software TREEVIEW Page 1996 4 4 7 Other files The gen file summarize a few statistics about the data such as
17. le in the default text editor The file can then be modified and saved The world must be rebuilt after a change in this file Button allowing to open the carrying capacity corresponding table see chapter 3 4 4 for a description of this table in the default text editor The file can then be modified and saved The world must be rebuilt after a change in this file CheckBox allowing a dynamic simulation see chapter 3 4 4 The world must be rebuilt after a change in this checkbox 3 3 4 Output parameters Some output parameters are placed in this panel because they need to be set prior to a simulation if one wants to automatically generate these outputs during the simulation These outputs are a temporal series of graphical representations of the state of a demographic parameter number of emigrants population densities or occupation Windows Bitmaps BMP or ASCII raster can be generated The output files are placed in two folders called respectively BMP and ASCII which are created in the same folder than the setting file The filename of each output file is composed by the name of the demographic variable followed by the number of generations at which it has been created Number of generations between each output files Beside the outputs for the intermediate states a series has always outputs for the initial and the final state of the simulation 14 16 Checkboxes for the generation of BMP files 17 19 Checkboxes for t
18. loci taken together Specific to DNA 9 Transition bias percentage of substitutions that are transitions Gamma a amount of heterogeneity in mutation rates along the sequence according to either a discrete or continuous gamma distribution Number of categories for DNA mutation variation Specific to Microsatellite Range constraint minimum and maximum size for microsatellite 4 2 3 Genetic data Different types of molecular data could be generated RFLP DNA Microsatellites and Standard each with its own specificities RFLP data Only a pure 2 allele model is implemented Several fully linked RFLP loci can be simulated assuming a homogeneous mutational process over all loci A finite sites model is used and mutations can hit the same site several times switching the RFLP site on and off We thus assume that there is the same probability for a site loss or for a site gain Microsatellite data We have implemented a pure stepwise mutation model SMM with or without constraint on the total size of the microsatellite Several fully linked microsatellite loci can be simulated under the same mutation model constraints The output for each loci is listed as a number of repeat having started arbitrarily at 10 000 repeats The number of repeats for each gene should thus be centered around that value DNA sequence data We have implemented here several simple finite sites mutational models The user can specify the percentage
19. mplesquare asc vegetation file dataSets_square simplesquare asc roughness topo file dataSets_square Dynamic_K txt Conversion table Vegetation gt K dataSets_square Dynamic_F txt Conversion table Vegetation gt F 3 demographic model 1 3 700 number of generations 3 generation time 10 growth rate 20 migration rate allow Initial Density overflow 0 1 static or dynamic environment 0 1 choice of friction type 0 vegetation l roughness topography 2 both dataSets_square genes_middle sam original genetic sample file 1 number of genetic simulations 10000 maximum number of simulated generations 0 Genetic Data Type 0 DNA 1 RFLP 2 MICROSAT 3 STANDARD 300 number of linked loci 0 001 total mutation rate 33 fraction of substitutions being transitions for DNA Gamma A for DNA mutation variation number of Categories for DNA mutation variation Range Constrainst for microsatellite generate Arlequin file Paup files or both 0 1 2 00 tau value generate migration BMP generate density BMP generate occupation BMP generate migration ASCII generate density ASCII generate occupation ASCII OPA OH Or Or 0 0 OVO 3 4 3 ASCII format for environmental data The environmental datasets that can be loaded into SPLATCH must be in ASCII raster format Two different datasets can be loaded The first one is the vegetation dataset definin
20. needed The two main files which are set through the settings files are typically called Dynamic_K txt and Dynamic_F txt On the first line of each of this file appears the number of changes during a simulation Then each line one per change is composed by the time of change in generations the filename of the corresponding table see below and an arbitrary description The three components of each line must be separated by a blank space For a non dynamic simulation only the first filename is considered regardless of the number indicated on the first line Example of Dynamic_K txt file 2 0 dataSets_africa veg2K txt vegetation at time 0 500 dataSets_africa veg2K_500 txt doubling of vegetation at time 500 Each file name must target a valid conversion table that makes the link between a particular vegetation or land cover category and a carrying capacity or friction value A conversion table is composed of a vegetation category number followed by a carrying capacity or friction value and by a description The vegetation category numbers must correspond to the numbers found in the input vegetation dataset see previous chapter 10 SPLATCHE v1 1 User Manual Example of veg2K txt file Tropical_rainforest Monsoon_or_dry_forest Tropical_woodland Tropical_scrub Tropical_semi_desert Tropical_grassland Tropical_extreme_desert 50 Savanna Broadleaved_temperate_evergreen_forest Montane_tropical_fores
21. of substitutions that are transitions the transition bias the amount of heterogeneity in mutation rates along a DNA sequence according to either a discrete or continuous Gamma distribution We can therefore simulate DNA sequences under a Jukes and Cantor model Jukes and Cantor 1969 or under a Kimura 2 parameter model Kimura 1980 with or without Gamma correction for heterogeneity of mutation rates Jin and Nei 1990 Other mutation models that depend on the nucleotide composition of the sequence were not considered here because of their complexity and because they require specifying many additional parameters like the mutation transition matrix and the equilibrium nucleotide composition 18 SPLATCHE v1 1 User Manual Standard data Following the definition given in Arlequin User Manual Schneider et al 2000 this type defines data for which the molecular basis is not particularly defined such as mere allele frequencies The comparison between alleles is done at each locus For each locus the alleles could be either similar or different 4 3 Input files 4 3 1 Genetic samples A file with the extansion sam allows to specify the localization of the sampled populations as well as the number of genes sampled in each population On the first line of this file the user specifies the number integer of sampled populations The second line is reserved for the legends Then each line defines a sample with 4 fields separated by
22. population is kept at a size equal to the Resize parameter After that time all 7 SPLATCHE v1 1 User Manual remaining lineages are put in a single deme of size 100 until the ultimate coalescent event A Unique origin Tay N N Resize 100 Time B Multi origins N Resize 3 Figure 3 2 Scheme of the unique or multiple origins models 3 4 2 Settings file VERSION 1 1 this setting file has changed and is not backward compatible with SPLATCHE 1 0 All parameters unless generation time and tau can be defined using the graphical interface of SPLATCHE However it is possible to save parameters into a new settings file so that they can be recovered later Only the graphical parameters are not contained in the settings files An example of settings files is provided with SPLATCHE settings _square txt with the corresponding data files in the folder called dataSets_square The example file is a simple square world constituted by 50x50 demes see Ray et al 2003 The setting file is composed of 31 parameters An example corresponding to settings _square txt is given below Each line starts with the value of the parameter followed by a blank a double slash and then the description of the parameter Parameters in bold indicate new parameters compared to SPLATCHE v 1 0 SPLATCHE v1 1 User Manual dataSets_square dens_init_tau txt pop source file dataSets_square si
23. resh rate number of generation numbers after which the display window is updated SRE Zoom factor of the display window 16 SPLATCHE v1 1 User Manual SPLATCHE 5 x General Settings Demographic outputs Genetic simulations Genetic samples file dataSets_square genes_middle sam l Browse M Mutation model specificities Data type DNA 6 No of linked loci 5 Total mutation rate por g ransition fraction 0 33 af 912 No of rate categories fi Output files Coalescences simulation 14 Arlequin Nexus Both I Coalescent tree simulation No of simulations 1 2 i no of simulated generations 5000 Refresh rate 1 Zoom factor fe Do simulations Current time D i S p ay 156 Active demes Wi n d OWS 51 Remaining lineages 55 Coalescent events 145 Migration events 5723 Status gt 1 Simulations Running Figure 4 1 Genetic module panel Demes where at least one gene is present appear in violet 4 2 2 Mutation model specificities For all kind of data Type of genetic data to be generated It could be DNA RFLP Microsatellite or Standard See Genetic data type Section for more details Number of fully linked loci to simulate It corresponds to the sequence length for 217 SPLATCHE v1 1 User Manual DNA Mutation rate per generation for all
24. t Open_boreal_woodlands Semi_arid_temperate_woodland Tundra i 2 3 4 5 6 7 8 By having several corresponding tables for the carrying capacity and or the friction values it is then possible to simulate complex changes of the environment through time ll SPLATCHE v1 1 User Manual 3 5 Graphical outputs window Graphical Outputs Display Windows Display Density e Migaiol g Zoom Nb active cells 2500 Density Nb rows 5 Row Nb columns 5 Col A Save to B 0 5 2 6 3 Occupation CEE EEE EE CEE CEE EEE GG CEE EC 6 Color Choice 3 C Gi DRAW Carr Cap Arrival time Figure 3 3 Graphical Outputs panel The numbers correspond to a description in the text Legend for the current display Buttons allowing to save the legend as a bitmap Radio button for the choice of color or shades of gray display 2 SPLATCHE v1 1 User Manual Information on the number of active cells cells having information for the vegetation the number of rows and the number of columns Information on the density the number of rows and the number of columns when the mouse cursor is over a particular deme Number of generations for the current display Zoom for the current display Radio button to choose among displaying the density the number of emigrants or the occupation black if occupied Button allowing to sa
25. t they needs to be in the same units that the coordinates defined in the header of the environmental files 5 Resize parameter it is the size of the population source before the beginning of the expansion This parameter is used only for genetic simulations If this parameter is set to 0 then the size of the population source before the onset of the expansion is regarded as being equal to the initial size parameter 2 In case initial density overflow is switch on the Resize parameter must be set to the total size of the initial population e g 2 000 if the user wants to keep this initial size before the beginning of the expansion 6 Migration rate from origin this parameter is only used with genetic simulations when there more than one origin It is the emigration rate from the current origin to the other origin s during the time prior to the expansion It is also equivalent to the probability of a lineage emigrating from the current origin When a lineage emigrate toward more than one origin it is dispatched randomly to one of the target origins Two examples of initial density files with 1 or 2 origins 1 middle 100 T3 0 0 1 Name Size Long Resize Migr 2 corner 100 13 0 middle 100 5 0 Name Size Long Resize 0 0 1 2 Migr Figure 3 2 shows a scheme of the simulation process with one or three origins The parameter Tau set trough the settings file indicates the duration in years during which the
26. the mean coalescence times the mean number of pairwise differences within and among demes and the mean length of the trees 5 Acknowledgements We are grateful to Stefan Schneider and Pierre Berthier for their computing assistance The development of the SPLATCHE program was possible through a Swiss NSF grant n 31 054059 98 6 Download sites SPLATCHE http cmpg unibe ch software splatche SIMCOAL http cmpg unibe ch software simcoal ARLEQUIN http cmpg unibe ch software arlequin TREEVIEW http taxonomy zoology gla ac uk rod treeview html PAUP http paup csit fsu edu 7 References Currat M 2004 Effets des expansions des populations humaines en Europe sur leur diversit g n tique D partement d Anthropologie et d Ecologie Gen ve Universit de Gen ve available at http www unige ch cyberdocuments theses2004 CurratM meta html Currat M N Ray et al 2004 SPLATCHE a program to simulate genetic diversity taking into account environmental heterogeneity Molecular Ecology Notes 4 1 139 142 Donnelly P and S Tavar 1995 Coalescents and genealogical structure under neutrality Annu Rev Genet 29 401 421 Ewens W J 1990 Population Genetics Theory The Past and the Future Mathematical and Statistical developments of Evolutionary Theory S Lessar Dordrecht Kluwer Academic Publishers 177 227 Excoffier L J Novembre et al 2000 SIMCOAL A general coalescent program
27. ve the current display as a bitmap o Cursor allowing to change the current generation and the display at the chosen generation pi pe eS yee Ea EN TS Buttons allowing to display the initial at generation 0 carrying capacity map the initial friction map and the proportional arrival time in each deme aie SPLATCHE v1 1 User Manual 3 6 Demographic outputs window This window allows to explore the demographic database that has been generated through a simulation SPLATCHE 10 x General Settings Demographic outputs Genetic simulations Selected deme a Selected row A Selected column 8 Demographic history Migration Hed 3 Number of individuals per generation Number of individuals 0 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500 Generation E Save to WMF 4 Selectors allowing to change the row and the column which will select the correct deme and display the history of the number of individuals density Graph showing the history of the number of individuals density for the selected deme It is possible to zoom in and out in the graph by drawing rectangles with the mouse cursor left button down 14 SPLATCHE v1 1 User Manual Second panel showing the histories of the number of emigrants in the four directions 4 Button allowing to save the graph in Windows Metafile format 4 Genetic module 4 1 Principles
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